create_endpoint.yaml

name: Create Hub Ingest Endpoint

on:
  workflow_dispatch:
    inputs:
      username:
        description: 'Username for the endpoint'
        required: true
        type: string
      size:
        description: 'Storage size (e.g., 50Gi)'
        required: true
        type: string

env:
  BIOC_HUBSINGEST_PATH: "${{ github.workspace }}"

jobs:
  create-endpoint:
    runs-on: ubuntu-latest
    container:
      image: amazon/aws-cli:2.22.35
      env:
        BIOC_HUBSINGEST_PATH: "/hubsingest"
    steps:
      - name: Install required packages
        run: |
          yum update -y && yum install -y curl tar gzip openssl

      - name: save kubeconfig
        shell: bash
        run: mkdir -p ~/.kube && echo "${{ secrets.KUBECONFIG }}" > ~/.kube/config
      
      - name: Install Kubectl
        run: |
          curl -LO "https://storage.googleapis.com/kubernetes-release/release/v1.24.4/bin/linux/amd64/kubectl" && \
          chmod +x ./kubectl && \
          mv ./kubectl /usr/local/bin/kubectl && \
          kubectl version
      
      - name: Set up environment
        run: |
          USERNAME_LOWER=$(echo "${{ inputs.username }}" | tr '[:upper:]' '[:lower:]')
          USERNAME_UPPER=$(echo "${{ inputs.username }}" | tr '[:lower:]' '[:upper:]')
          echo "SECRET_NAME=S3KEY_${USERNAME_UPPER}" >> $GITHUB_ENV
          echo "USERNAME=${USERNAME_LOWER}" >> $GITHUB_ENV
      
      - name: Create endpoint then test
        run: |
          mkdir -p $BIOC_HUBSINGEST_PATH
          cd $BIOC_HUBSINGEST_PATH
          curl -O https://raw.githubusercontent.com/Bioconductor/hubsingest/devel/install_hubsingest.sh
          bash install_hubsingest.sh
          export PATH="$PATH:$BIOC_HUBSINGEST_PATH"
          hubsingest create_endpoint "${{ env.USERNAME }}" "${{ inputs.size }}" ${{ secrets[env.SECRET_NAME] }}
          kubectl wait -n "${{ env.USERNAME }}-ns" --for=condition=ready pod -l app=versitygw --timeout=300s
          kubectl wait -n "${{ env.USERNAME }}-ns" --for=condition=ready certificate ${{ env.USERNAME }}-hubsingest-bioconductor-org-key --timeout=600s || bash scripts/reset_endpoint_ssl.sh "${{ env.USERNAME }}" && kubectl wait -n "${{ env.USERNAME }}-ns" --for=condition=ready certificate ${{ env.USERNAME }}-hubsingest-bioconductor-org-key --timeout=600s
          sleep 30
          hubsingest test_endpoint "${{ env.USERNAME }}"